rbbt-GE 1.0.0 → 1.1.0

checksums.yaml

@@ -0,0 +1,15 @@
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data/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2010-2011 Miguel Vázquez García
+Copyright (c) 2010-2013 Miguel Vázquez García
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/lib/rbbt/GE.rb

@@ -5,8 +5,8 @@ module GE
   MA      = File.join(LIB_DIR, 'MA.R')
 
   def self.run_R(command)
-    cmd = "source('#{MA}');" << command
-    R.run(cmd)
+    cmd = "\nsource('#{MA}');\n" << command
+    R.run(cmd, :monitor => true)
   end
 
   def self.r_format(list, options = {})
@@ -35,5 +35,11 @@ module GE
     FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
     GE.run_R("rbbt.GE.process(#{ r_format datafile }, main = #{r_format(main, :strings => true)}, contrast = #{r_format(contrast, :strings => true)}, log2=#{ r_format log2 }, outfile = #{r_format outfile}, key.field = #{r_format key_field}, two.channel = #{r_format two_channel})")
   end
+
+  def self.barcode(datafile, outfile, factor = 2)
+    FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
+    GE.run_R("rbbt.GE.barcode(#{ r_format datafile }, #{ r_format outfile }, #{ r_format factor })")
+  end
+
 end
 

data/lib/rbbt/GE/GEO.rb

@@ -142,6 +142,7 @@ module GEO
     def self.parse_header(stream, info)
       header = ""
       while line = stream.readline
+        line = Misc.fixutf8 line
         header << line
         break if line =~ /^#{info[:DELIMITER]}/i
         raise "Delimiter not found" if stream.eof?

data/share/lib/R/MA.R

@@ -1,5 +1,35 @@
 library(limma)
 
+#########################################################################
+# BARCODE
+
+rbbt.GE.barcode <- function(matrix_file, output_file, sd.factor = 2){
+  data = rbbt.tsv(matrix_file)
+  data.mean = rowMeans(data, na.rm=T)
+  data.sd = apply(data, 1, sd, na.rm=T)
+  data.threshold = as.matrix(data.mean) + sd.factor * as.matrix(data.sd)
+  names(data.threshold) = names(data.mean)
+  rm(data.mean)
+  rm(data.sd)
+
+  file.barcode = file(output_file, 'w')
+
+  cat("#Ensembl Gene ID", file = file.barcode)
+  cat("\t", file = file.barcode)
+  cat(colnames(data), file = file.barcode, sep="\t")
+  cat("\n", file = file.barcode)
+     
+  for (gene in rownames(data)){
+    barcode = (data[gene,] - data.threshold[gene]) > 0
+
+    cat(gene, file = file.barcode)
+    cat("\t", file = file.barcode)
+    cat(barcode, file = file.barcode, sep = "\t")
+    cat("\n", file = file.barcode)
+  }
+  close(file.barcode)
+}
+
 #########################################################################
 # Model processing 
 
@@ -529,6 +559,4 @@ MA.load <- function(prefix, orders = TRUE, logratios = TRUE, t = TRUE, p.values
 
 
     return(data);
-
-
 }

metadata

@@ -1,20 +1,18 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-GE
 version: !ruby/object:Gem::Version
-  version: 1.0.0
-  prerelease: 
+  version: 1.1.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-21 00:00:00.000000000 Z
+date: 2013-10-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -22,7 +20,6 @@ dependencies:
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
@@ -39,32 +36,31 @@ files:
 - lib/rbbt/GE/GEO.rb
 - share/install/GEO/Rakefile
 - share/lib/R/MA.R
-- test/test_helper.rb
 - test/rbbt/GE/test_GEO.rb
+- test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-GE
 licenses: []
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Gene Expression in RBBT
 test_files:
-- test/test_helper.rb
 - test/rbbt/GE/test_GEO.rb
+- test/test_helper.rb